HDF5 History ============ This file contains development history of HDF5 1.8 branch 5. Release Information for hdf5-1.8.4 4. Release Information for hdf5-1.8.3 3. Release Information for hdf5-1.8.2 2. Release Information for hdf5-1.8.1 1. Release Information for hdf5-1.8.0 [Search on the string '%%%%' for per-release section breaks.] %%%%1.8.4%%%% HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.3 and HDF5 1.8.4, and contains information on the platforms tested and known problems in HDF5-1.8.4 For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.4 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.4 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.4 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.4 (current release) versus Release 1.8.3": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.3 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Configuration suite now uses Automake 1.11 and Autoconf 2.64. MAM 2009/08/31. - Changed default Gnu fortran compiler from g95 to gfortran since gfortran is more likely installed with gcc now. -AKC 2009/07/19- Library ------- - The embedded library information is displayed by H5check_version() if a version mismatch is detected. Also changed H5check_version() to suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 or higher. (Old behavior treated 3 or higher the same as 1, that is print a warning and allows the program to continue. (AKC - 2009/9/28) - If a user does not care for the extra library information insert in the executables, he may turn it off by --disable-embedded-libinfo during configure. (AKC - 2009/9/15) Parallel Library ---------------- - None Tools ----- - h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect) before call ABS(...) at h5diff_array.c. This will make that (INF==INF) is true (INF is treated as an number instead of NaN) (PC -- 2009/07/28) - h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON). Change default to use strict equality (PC -- 2009/09/12) High-Level APIs --------------- - None F90 API ------- - Added H5Oopen_by_addr_f MSB - 9/14/09 C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - PathScale compilers are recognized and can build the HDF5 library properly. AKC - 2009/7/28 - Bug Fixes since HDF5-1.8.3 ========================== Configuration ------------- - Removed the following config files, as we no longer support them: config/dec-osf*, config/hpux11.00, config/irix5.x, config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* MAM - 2009/10/08 - Modified configure and make process to properly preserve user's CFLAGS (and company) environment variables. Build will now properly use automake's AM_CFLAGS for any compiler flags set by the configure process. Configure will no longer modify CFLAGS directly, nor will setting CFLAGS during make completely replace what configure has set up. MAM - 2009/10/08 - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS machine has long retired. AKC - 2009/10/06. - Added $(EXEEXT) extension to H5detect when it's executed in the src/Makefile to generate H5Tinit.c so it works correctly on platforms that require the full extension when running executables. MAM - 2009/10/01 - BZ #1613 - Configure will now set FC and CXX to "no" when fortran and c++ are not being compiled, respectively, so configure will not run some of the compiler tests for these languages when they are not being used. MAM - 2009/10/01 - The --enable-static-exec flag will now properly place the -static flag on the link line of all installed executables. This will force the executable to link with static libraries over shared libraries, provided the static libraries are available. MAM - 2009/08/31 - BZ #1583 - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - Library ------- - Fixed a bug where writing and deleting many global heap objects (i.e. variable length data) would render the file unreadable. Previously created files exhibiting this problem should now be readable. NAF - 2009/10/27 - 1483 - Fixed error in library's internal caching mechanisms which could cause an assertion failure (and attendent core dump) when encountering an unusually formatted file. (QAK - 2009/10/13) - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628 - Fixed an assertion failure that occurred when H5Ocopy was called on a dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597 - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. NAF - 2009/09/25 - 1620 - Fixed a bug where properties weren't being compared with the registered compare callback. NAF - 2009/09/25 - 1555 - Corrected problem where library would re-write the superblock in a file opened for R/W access, even when no changes were made to the file. (QAK - 2009/08/20, Bz#1473) - Fixed a bug where H5Pget_filter_by_id would succeed when called for a filter that wasn't present. NAF - 2009/06/25 - 1250 - Fixed an issue with committed compound datatypes containing a vlen. Also fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593 Parallel Library ---------------- - None Tools ----- - h5dump/h5ls display buffer resize fixed in tools library. ADB - 2009/7/21 - 1520 - perf_serial test added to Windows projects and check batch file. ADB - 2009/06/11 -1504 F90 API ------ - Fixed bug in h5lget_info_by_idx_f by adding missing arguments, consequently changing the API. New API is: SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, & link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id) MSB - 2009/9/17 - 1652 - Corrected the values for the H5L_flags FORTRAN constants: H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F MSB - 2009-09-17 - 1653 - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F MSB - 2009-9-24 - 1471 C++ API ------ - None High-Level APIs: ------ - Fixed a bug where the H5TB API would forget the order of fields when added out of offset order. NAF - 2009/10/27 - 1582 - H5DSis_attached failed to account for different platform types. Added a get native type call. ADB - 2009/9/29 - 1562 Fortran High-Level APIs: ------ - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 (LLNL Up) xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (SNL red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.3.5 20091004 g++ 4.3.5 20091004 gfortran 4.3.5 20091004 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.2 20091006 g++ 4.4.2 20091006 gfortran 4.4.2 20091006 Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) (jam) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) PGI C, Fortran, C++ 8.0-5 32-bit PGI C, Fortran, C++ 8.0-1 32-bit Intel(R) C Compiler for 32-bit applications, Versions 11.0, 11.1 Intel(R) C++ Compiler for 32-bit applications, Version 11.0, 11.1 Intel(R) Fortran Compiler for 32-bit applications, Version 11.0, 11.1 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.0.8 compiled with gcc (GCC) 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) (amani) tested for both 32- and 64-bit binaries Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Versions 11.1. PGI C, Fortran, C++ Version 9.0-4 for 64-bit target on x86-64 gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017 SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.38 SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30 (linew) Sun Fortran 95 8.3 SunOS_sparc Patch 127000-11 2009/10/06 Sun C++ 5.9 SunOS_sparc Patch 124863-16 2009/09/15 Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 perfctr #6 SMP Open MPI 1.2.2 (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 #1 SMP ia64 Intel(R) C++ Version 8.1.037 (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 10.1. (SNL Thunderbird) Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (SNL Glory) Versions 10.1. Windows XP Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1 MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release C = Cluster W = Workstation x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n(4) y y y Windows XP x64 n y(4) n(4) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y RedHat EL5 2.6.18-164 i686 Intel W n y n y y n RedHat EL5 2.6.18-164 i686 PGI W n y n y y n RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n RedHat EL5 2.6.18-164 x86_64 PGI W n y n y y y SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n SuSe Linux 2.4.21 ia64 Intel C y y y y y n Cray XT3 2.0.62 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y y Windows XP x64 y y(4) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.3-STABLE 32&64 bit y y y y RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y RedHat EL5 2.6.18-164 i686 Intel W y y y n RedHat EL5 2.6.18-164 i686 PGI W y y y n RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y RedHat EL5 2.6.18-164 x86_64 IntelW y y y n RedHat EL5 2.6.18-164 x86_64 PGI W y y y n SuSe Linux 2.6.16 SGI Altix ia64 C y n RedHat EL4 2.6.18 Xeon Lustre C y y y n SuSe Linux 2.4.21 ia64 Intel C y y y n Cray XT3 2.0.62 n n n n (1) Fortran compiled with g95. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2005 or Cygwin Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * Parallel mode in AIX will fail some of the testcheck_version.sh tests where it treats "exit(134) the same as if process 0 had received an abort signal. This is fixed and will be available in the next release. AKC - 2009/11/3 * Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. The error is due to insufficient memory requested. Request a large amount of runtime memory by setting the following environment variable for more memory. LDR_CNTRL=MAXDATA=0x20000000@DSA AKC - 2009/10/31 * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not existing. This is due to the MPI_File_open() call failing if the amode has the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * There is a known issue in which HDF5 will change the timestamp on a file simply by opening it with read/write permissions, even if the file is not modified in any way. This is due to the way in which HDF5 manages the file superblock. A fix is currently underway and should be included in the 1.8.4 release of HDF5. MAM - 2009/04/28 * For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is produced. If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. %%%%1.8.3%%%% HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.2 and HDF5 1.8.3, and contains information on the platforms tested and known problems in HDF5-1.8.3. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.3 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.3 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.3 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.3 (current release) versus Release 1.8.2": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.2 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Added libtool version numbers to generated c++, fortran, and hl libraries. MAM 2009/04/19. - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. - Added a Make target of check-all-install to test the correctness of installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 Library ------- - Embed the content of libhdf5.settings into the hdf5 executables so that an "orphaned" executables can display (via the Unix strings command, for example) the library settings used to build the executables. This is a prototype implementation. Improvement will be added in next release. AKC - 2009/04/20 - Separated "factory" free list class from block free lists. These free lists are dynamically created and manage blocks of a fixed size. H5set_free_list_limits() will use the same settings specified for block free lists for factory free lists. NAF - 2009/04/08 - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29 - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a user-defined callback function for external link traversal. NAF - 2009/01/08 - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to allow the user to specify the file access flags used to open the target file of an external link. NAF - 2009/01/08 - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow individual rdcc configuration for each dataset. Added H5Dget_access_plist() function to retrieve a dataset access property list from a dataset. NAF - 2008/11/12 - Added H5Iis_valid() function to check if an id is valid without producing an error message. NAF - 2008/11/5 - Added code to maintain a min_clean_fraction in the metadata cache when in serial mode. MAM - 2009/01/9 Parallel Library ---------------- - Modified parallel tests to run with arbitrary number of processes. The modified tests are testphdf5 (parallel dataset access), t_chunk_alloc (chunk allocation), and t_posix_compliant (posix compliance). The rest of the parallel tests already use in the code the number of processes available in the communicator. (CMC - 2009/04/28) Tools ----- - h5diff new flag, -c, --compare, list objects that are not comparable. PVN - 2009/4/2 - 1368 - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2 - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519 - h5repack now handles group creation order. PVN - 2009/4/2 - 1402 - h5repack: When user doesn't specify a chunk size, h5repack now defines a default chunk size as the same size of the size of the hyperslab used to read the chunks. The size of the hyperslabs are defined as the size of each dimension or a predefined constant, whatever is smaller. This assures that the chunk read fits in the chunk cache. PVN - 2008/11/21 High-Level APIs --------------- - Table: In version 3.0 of Table, the writing of the "NROWS" attribute (used to store number of records) was deprecated. PVN - 2008/11/24 F90 API ------- - Added for the C APIs the Fortran wrappers: h5dget_access_plist_f h5iis_valid_f h5pset_chunk_cache_f h5pget_chunk_cache_f MSB - 2009/04/17 C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== Bug Fixes since HDF5-1.8.2 ========================== Configuration ------------- - The --includedir=DIR configuration option now works as intended, and can be used to specify the location to install C header files. The default location remains unchanged, residing at ${prefix}/include. MAM - 2009/03/10 - BZ #1381 - Configure no longer removes the '-g' flag from CFLAGS when in production mode if it has been explicitly set in the CFLAGS environment variable prior to configuration. MAM - 2009/03/09 - BZ #1401 Library ------- - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 API. NAF - 2009/04/20 - 1533 - Fixed a problem with using data transforms with non-native types in the file. NAF - 2009/04/20 - 1548 - Added direct.h include file to windows section of H5private.h to fix _getcwd() warning. ADB - 2009/04/14 - 1536 - Fixed a bug that prevented external links from working after calling H5close(). NAF - 2009/04/10 - 1539 - Modified library to write cached symbol table information to the superblock, to allow library versions 1.3.0 to 1.6.3 to read files created by this version. NAF - 2009/04/08 - 1423 - Changed skip lists to use a deterministic algorithm. The library should now never call rand() or srand(). NAF - 2009/04/08 - 503 - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups when that property was set. NAF - 2009/04/07 - 1526 - Fixed a bug that caused files with a user block to grow by the size of the user block every time they were opened. NAF - 2009/03/26 - 1499 - Fixed a rare problem that could occur with files using the old (pre 1.4) array datatype. NAF - 2009/03/23 - Modified library to be able to open files with corrupt root group symbol table messages, and correct these errors if they are found. Such files can only be successfully opened with write access. NAF - 2009/03/23 - 1189 - Removed the long_long #define and replaced all instances with "long long". This caused problems with third party products. All currently supported compliers support the type. ADB - 2009/03/05 - Fixed various bugs that could prevent the fill value from being written in certain rare cases. NAF - 2009/02/26 - 1469 - Fixed a bug that prevented more than one dataset chunk from being cached at a time. NAF - 2009/02/12 - 1015 - Fixed an assertion failure caused by opening an attribute multiple times through multiple file handles. NAF - 2009/02/12 - 1420 - Fixed a problem that could prevent the user from adding attributes (or any object header message) in some circumstances. NAF - 2009/02/12 - 1427 - Fixed a bug that could cause problems when an attribute was added to a committed datatype using the committed datatype's datatype. NAF - 2009/02/12 - Fixed a bug that could cause problems when copying an object with a shared message in its own object header. NAF - 2009/01/29 - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes. NAF - 2009/01/27 - 1443 - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise packed compound type. NAF - 2009/01/14 - Fixed up some old v2 btree assertions that get run in debug mode that were previously failing on compilation, and removed some of the more heavily outdated and non-rewritable ones. MAM - 2008/12/15 - Fixed a bug that could cause problems when "automatically" unmounting multiple files. NAF - 2008/11/17 - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. PVN - 2009/01/8 Parallel Library ---------------- - None Tools ----- - Fixed many problems that could occur when using h5repack with named datatypes. NAF - 2009/4/20 - 1516/1466 - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant defined as 1024Kb, such as array types with large dimensions. PVN - 2009/4/1 - 1501 - h5import: By selecting a compression type, a big endian byte order was being selected. PVN - 2009/3/11 - 1462 - zip_perf.c had missing argument on one of the open() calls. Fixed. AKC - 2008/12/9 F90 API ------ - None C++ API ------ - None High-Level APIs: ------ - Dimension scales: The scale index return value in H5DSiterate_scales was not always incremented. PVN - 2009/4/8 - 1538 Fortran High-Level APIs: ------ - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) was not correctly returning the dimension array PVN - 2009/3/23 Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 (LLNL Up) xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (SNL red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.3.4 20090419 g++ 4.3.4 20090419 gfortran 4.3.4 20090419 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.1 20090421 g++ 4.4.1 20090421 gfortran 4.4.1 20090421 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (jam) PGI C, Fortran, C++ 7.2-1 32-bit PGI C, Fortran, C++ 8.0-1 32-bit Intel(R) C Compiler for 32-bit applications, Versions 10.1, 11.0 Intel(R) C++ Compiler for 32-bit applications, Version 10.1, 11.0 Intel(R) Fortran Compiler for 32-bit applications, Version 10.1, 11.0 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (kagiso) MPICH mpich2-1.0.8 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (smirom) Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Versions 10.1, 11.0. PGI C, Fortran, C++ Version 7.2-1, 8.0-1 for 64-bit target on x86-64 gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) tested for both 32- and 64-bit binaries Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.38 SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09 (linew) Sun WorkShop 6 update 2 Fortran 95 8.3 Patch 127000-07 Sun WorkShop 6 update 2 C++ 5.8 Patch 124863-11 Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026 perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026 (abe) Open MPI 1.2.2 MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 #1 SMP ia64 Intel(R) C++ Version 8.1.037 (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 9.1. (SNL Spirit) Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 10.1. (SNL Thunderbird) Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (SNL Glory) Versions 10.1. Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (LLNL Zeus) Versions 9.1. gcc/gfortran/g++ (GCC) 4.1.2. Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release C = Cluster W = Workstation x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n y y y y y Windows XP n y(4) n(4) y y y Windows XP x64 n y(4) n(4) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y RedHat EL5 2.6.18-128 i686 Intel W n y n y y n RedHat EL5 2.6.18-128 i686 PGI W n y n y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y SuSe Linux 2.6.16 x86_64 Intel W n y n y y n SuSe Linux 2.6.16 x86_64 PGI W n y n y y y SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n SuSe Linux 2.4.21 ia64 Intel C y y y y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y IRIX64_6.5 32-bit y dna y y IRIX64_6.5 64-bit y y n y Windows XP y y(4) y y Windows XP x64 y y(4) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.3-STABLE 32&64 bit y n y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y RedHat EL5 2.6.18-128 i686 Intel W y y y n RedHat EL5 2.6.18-128 i686 PGI W y y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y SuSe Linux 2.6.16 x86_64 Intel W y y y n SuSe Linux 2.6.16 x86_64 PGI W y y y n SuSe Linux 2.6.16 SGI Altix ia64 C y n RedHat EL4 2.6.18 Xeon Lustre C y y y n SuSe Linux 2.4.21 ia64 Intel C y y y n Cray XT3 2.0.41 n n n n (1) Fortran compiled with g95. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2005 or Cygwin Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * There is a known issue in which HDF5 will change the timestamp on a file simply by opening it with read/write permissions, even if the file is not modified in any way. This is due to the way in which HDF5 manages the file superblock. A fix is currently underway and should be included in the 1.8.4 release of HDF5. MAM - 2009/04/28 * For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is produced. If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases: 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, change the following line in your code H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platforms for serial mode. The parallel mode works fine with this option. It is suggested that you do not use this option on these platforms during configuration. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. %%%%1.8.2%%%% HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2, and contains information on the platforms tested and known problems in HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.2 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.2 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.2 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.2 (current release) versus Release 1.8.1": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.8.1 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15). Library ------- - Added two new public routines: H5Pget_elink_fapl() and H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) - Improved free space tracking in file to be faster. (QAK - 2008/10/06) - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) Parallel Library ---------------- - None Tools ----- - h5repack: added new options -u and -b to add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) - h5repack: added options -t and -a to call H5Pset_alignment while creating a repacked file. (PVN - 2008/08/29) - h5ls: added capability to traverse through external links when the -r (recursive) flag is given. (NAF - 2008/09/16) - h5ls: added -E option to enable traversal of external links. h5ls will not traverse external links without this flag being set. (NAF - 2008/10/06) - h5dump: when -b flag is used without a keyword after it, binary output defaults to NATIVE. MEMORY keyword was deprecated and replaced by NATIVE keyword. (PVN - 2008/10/30) - h5diff: returns 1 when file graphs differ by any object. Error return code was changed to 2 from -1. (PVN - 2008/10/30) - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP instead (PVN - 2008/10/30) F90 API ------ - Added optional parameter 'mounted' to H5Gget_info_f, H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24) - Added H5Tget_native_type_f (MSB - 2008/09/30) C++ API ------ - These member functions were added as wrapper for H5Rdereference to replace the incorrect IdComponent::dereference(). void H5Object::dereference(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(H5File& h5file, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(Attribute& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) In addition, these constructors were added to create the associated objects by way of dereference: DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) (BMR - 2008/10/29) Support for New Platforms, Languages, and Compilers =================================================== - Intel 10.1 is supported on Mac OS X 10.5.4. Note: When Fortran is enabled, configure automatically disables the build of shared libraries (i.e., only static C and C++ HDF5 libraries will be built along with the static HDF5 Fortran library). Intel 10.1 C and C++ compilers require "-no-multibyte-chars" compilation flag due to the known bug in the compilers. (EIP - 2008/10/30) Bug Fixes since HDF5-1.8.1 ========================== Configuration ------------- - Fixed error with 'make check install' failing due to h5dump needing other tools built first. (MAM - 2008/10/15). - When using shared szip, it is no longer necessary to specify the path to the shared szip libraries in LD_LIBRARY_PATH. (MAM - 2008/10/15). - The file libhdf5_fortran.settings is not installed since its content is included in libhdf5.settings now. (AKC - 2008/10/21) - "make DESTDIR=xxx install" failed to install some tools and files (e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8). Library ------- - H5Ovisit and H5Ovisit_by_name will now properly terminate when the callback function returns a positive value on the starting object. (NAF - 2008/11/03) - Fixed an error where a null message could be created that was larger than could be written to the file. (NAF - 2008/10/23) - Corrected error with family/split/multi VFD not updating driver info when "latest" version of the file format used. (QAK - 2008/10/14) - Corrected alignment+threshold errors to work correctly when metadata aggregation is enabled. (QAK - 2008/10/06) - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered by the library for internal library use. (NAF - 2008/10/06) - Fixed potential memory leak during compound conversion. (NAF - 2008/10/06) - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26) - Fixed an issue that could cause data to be improperly overwritten during compound type conversion. (NAF - 2008/09/19) - Fixed pointer alignment violations that could occur during vlen conversion. (NAF - 2008/09/16) - Fixed problem where library could cause a segmentation fault when an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) - Fixed improper shutdown when objects have reference count > 1. The library now tracks reference count due to the application separately from that due to internal library routines. (NAF - 2008/08/19) - Fixed assertion failure caused by incorrect array datatype version. (NAF - 2008/08/08) - Fixed an issue where mount point traversal would fail when using multiple handles for the child. (NAF - 2008/08/07) - Fixed an issue where mount points were inaccessible when using multiple file handles for the parent. The mount table is now in the shared file structure (the parent pointer is still in the top structure). (NAF - 2008/08/07) - Fixed assertion failure caused by incorrect array datatype version. (NAF - 2008/08/04) - Fixed issue where a group could have a file mounted on it twice. (QAK - 2008/07/15) - When an attribute was opened twice and data was written with one of the handles, the file didn't have the data. It happened because each handle had its own object structure, and the empty one overwrote the data with fill value. This is fixed by making some attribute information like the data be shared in the attribute structure. (SLU - 2008/07/07) - Fixed a Windows-specific issue in the ohdr test which was causing users in some timezones to get false errors. This a deficiency in the Windows mktime() function, and has been handled properly. (SJW - 2008/06/19) Parallel Library ---------------- - None Tools ----- - h5dump now checks for uniqueness of committed datatypes. (NAF - 2008/10/15) - Fixed unnecessary indentation of committed datatypes in h5dump. (NAF - 2008/10/15) - Fixed bugs in h5stat: segmemtation fault when printing groups and print warning message when traversal of objects is unsuccessful. (see bug #1253) (VC- 2008/10/13) - Fixed bug in h5ls that prevented relative group listings (like "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) - h5dump: when doing binary output (-b), the stdout printing of attributes was done incorrectly. Removed printing of attributes when doing binary output. (PVN - 2008/06/05) F90 API ------ - h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND and H5S_SELECT_PREPEND (MSB - 2008/09/30) - h5sget_select_elem_pointlist: Fixed list of returned points by rearranging the point list correctly by accounting for C conventions. (MSB - 2008/09/30) - h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension of arrays.(MSB - 2008/9/30) - h5sget_select_bounds_f: Swapped array bounds to account for C and Fortran reversed array notation (MSB - 2008/9/30) - Changed to initializing string to a blank character instead of a null type in tH5P.f90 to fix compiling error using AIX 5.3.0 (MSB - 2008/7/29) - Fixed missing commas in H5test_kind.f90 detected by NAG compiler (MSB - 2008/7/29) - Fixed passing and array to a scalar in tH5A_1_8.f90 detected by NAG compiler (MSB - 2008/7/29) - Added the ability of the test programs to use the status of HDF5_NOCLEANUP to determine if the *.h5 files should be removed or not after the tests are completed (MSB - 2008/10/1) - In nh5tget_offset_c: (MSB 9/12/2008) If offset was equal to 0 it returned the error code of -1, this was changed to return an error code of -1 when the offset value is < 0. - Uses intrinsic Fortran function SIZEOF if available when detecting type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3) - Put the DOUBLE PRECISION interfaces in a separate module and added a USE statement for the module. The interfaces are included/excluded depending on the state of FORTRAN_DEFAULT_REAL is DBLE_F which detects if the default REAL is DOUBLE PRECISION. This allows the library to be compiled with -r8 Fortran flag without the user needing to edit the source code. (MSB - 200/8/27) - Enable building shared library for fortran by adding the flag -fPIC to the compile flags for versions of Intel Fortran compiler >=9 (MSB - 2008/8/26) C++ API ------ - Fixed a design bug which allowed an Attribute object to create/modify attributes (bugzilla #1068). The API class hierarchy was revised to address the problem. Classes AbstractDS and Attribute are moved out of H5Object. Class Attribute now multiply inherits from IdComponent and AbstractDs and class DataSet from H5Object and AbstractDs. In addition, the data member IdComponent::id was moved into subclasses: Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. (BMR - 2008/05/20) - IdComponent::dereference was incorrect and replaced as described in "New Features" section. (BMR - 2008/10/29) Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007) (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit Intel(R) C Compiler for 32-bit applications, Version 10.1 Intel(R) C++ Compiler for 32-bit applications, Version 10.1 Intel(R) Fortran Compiler for 32-bit applications, Version 10.1 Absoft 32-bit Fortran 95 10.0.4 MPICH mpich-1.2.7 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.6p1 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T SMP x86_64 GNU/Linux Ver. 10.1.013 (smirom) Intel(R) Fortran Intel(R) EM64T Ver. 10.1.013 PGI C, Fortran, C++ Version 7.2-1 for 64-bit target on x86-64 MPICH mpich-1.2.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) tested for both 32- and 64-bit binaries Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.16 SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 Sun WorkShop 6 update 2 C++ 5.8 Patch 121019-06 Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) Intel(R) C++ Version 10.0.026 Intel(R) Fortran Compiler Version 10.0.026 Open MPI 1.2.2 MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 #1 SMP ia64 gcc (GCC) 3.2.2 (NCSA tg-login) Intel(R) C++ Version 8.1.037 Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) gcc 3.4.6 20060404 Intel(R) C++ Version 10.0 Intel (R) Fortran Compiler Version 10.0 mvapich2-0.9.8p2patched-intel-ofed-1.2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n y y y y y Windows XP n y(15) n(15) y y y Windows XP x64 n y(15) n(15) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 (3) W y(1) y(10) y(1) y y y RedHat EL4 Intel (3) W n y n y y n RedHat EL4 PGI (3) W n y n y y n SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y SuSe x86_64 Int(3,12) W n y(13) n y y n SuSe x86_64 PGI(3,12) W n y(8) n y y y Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Linux 2.6 RHEL C Lustre Intel (5) y(4) y y(4) y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y IRIX64_6.5 32-bit y dna y y IRIX64_6.5 64-bit y y n y Windows XP y y(15) y y Windows XP x64 y y(15) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.2 32&64 bit y n y y RedHat EL4 (3) W y y(10) y y RedHat EL4 Intel (3) W y y y n RedHat EL4 PGI (3) W y y y n SuSe x86_64 GNU(3,12) W y y y y SuSe x86_64 Int(3,12) W y y y n SuSe x86_64 PGI(3,12) W y y y n Linux 2.4 SuSE C ia64 C Intel (7) y y y n Linux 2.4 SGI Altix C ia64 Intel y n Linux 2.6 RHEL C Lustre Intel (5) y y y n Cray XT3 2.0.41 n n n n Notes: (1) Using mpich2 1.0.6. (2) Using mpich2 1.0.7. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Using mvapich2 0.9.8. (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 (9) With Compaq Visual Fortran 6.6c compiler. (10) With PGI and Absoft compilers. (11) PGI and Intel compilers for both C and Fortran (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases: 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, change the following line in your code H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platforms for serial mode. The parallel mode works fine with this option. It is suggested that you do not use this option on these platforms during configuration. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. %%%%1.8.1%%%% HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between the HDF5-1.8.1 release and HDF5 1.8.0, and contains information on the platforms tested and known problems in HDF5-1.8.1. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.1 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.1 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.1 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.1 (current release) versus Release 1.8.0": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.8.0 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - The lib/libhdf5.settings file contains much more configure information. (AKC - 2008/05/18) - The new configure option "--disable-sharedlib-rpath" disables embedding the '-Wl,-rpath' information into executables when shared libraries are produced, and instead solely relies on the information in LD_LIBRARY_PATH. (MAM - 2008/05/15) - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and Libtool 2.2.2 (MAM - 2008/05/01) Source code distribution ======================== Library ------- - None Parallel Library ---------------- - None Tools ----- - h5repack: Reinstated the -i and -o command line flags to specify input and output files. h5repack now understands both the old syntax (with -i and -o) and the new syntax introduced in Release 1.8.0. (PVN - 2008/05/23) - h5dump: Added support for external links, displaying the object that an external link points to. (PVN - 2008/05/12) - h5dump: Added an option, -m, to allow user-defined formatting in the output of floating point numbers. (PVN - 2008/05/06) - h5dump, in output of the -p option: Added effective data compression ratio to the dataset storage layout output when a compression filter has been applied to a dataset. (PVN - 2008/05/01) F90 API ------ New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were added. See "Release 1.8.1 (current release) versus Release 1.8.0" in the document "HDF5 Software Changes from Release to Release" (http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the complete list of the new APIs. C++ API ------ - None Support for New Platforms, Languages, and Compilers =================================================== - Both serial and parallel HDF5 are supported for the Red Storm machine which is a Cray XT3 system. - The Fortran library will work correctly if compiled with the -i8 flag. This has been tested with the g95, PGI and Intel Fortran compilers. Bug Fixes since HDF5-1.8.0 ========================== Configuration ------------- - None Source code distribution ======================== Library ------- - Chunking: Chunks greater than 4GB are disallowed. (QAK - 2008/05/16) - Fixed the problem with searching for a target file when following an external link. The search pattern will depend on whether the target file's pathname is an absolute or a relative path. Please see the H5Lcreate_external description in the "HDF5 Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html). (VC - 2008/04/08) - Fixed possible file corruption bug when encoding datatype descriptions for compound datatypes whose size was between 256 and 511 bytes and the file was opened with the "use the latest format" property enabled (with H5Pset_libver_bounds). (QAK - 2008/03/13) - Fixed bug in H5Aget_num_attrs() routine to correctly handle an invalid location identifier. (QAK - 2008/03/11) Parallel Library ---------------- - None Tools ----- - Fixed bug in h5diff that prevented datasets and attributes with variable-length string elements from comparing correctly. (QAK - 2008/02/28) - Fixed bug in h5dump that caused binary output to be made only for the first dataset, when several datasets were requested. (PVN - 2008/04/07) F90 API ------ - The h5tset(get)_fields subroutines were missing the parameter to specify a sign position; fixed. (EIP - 2008/05/23) - Many APIs were fixed to work with the 8-byte integers in Fortran vs. 4-byte integers in C. This change is trasparent to user applications. C++ API ------ - The class hierarchy was revised to address the problem reported in bugzilla #1068, Attribute should not be derived from base class H5Object. Classes AbstractDS was moved out of H5Object. Class Attribute now multiply inherits from IdComponent and AbstractDs and class DataSet from H5Object and AbstractDs. In addition, data member IdComponent::id was moved into subclasses: Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. (BMR - 2008/05/20) - IdComponent::dereference was incorrect; it was changed from: void IdComponent::dereference(IdComponent& obj, void* ref) to: void H5Object::dereference(H5File& h5file, void* ref) void H5Object::dereference(H5Object& obj, void* ref) (BMR - 2008/05/20) - Revised Attribute::write and Attribute::read wrappers to handle memory allocation/deallocation properly. (bugzilla 1045) (BMR - 2008/05/20) Platforms Tested ================ The following platforms and compilers have been tested for this release. Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 mpicc 1.0.2 mpif90 1.0.2 FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20070620 FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20080123 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9 (RHEL4) Intel 10.0 compilers (abe.ncsa.uiuc.edu) Linux 2.4.21-47 gcc 3.2.3 20030502 (osage) Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3) (kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC) Intel 9.1 (icc, ifort, icpc) Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, (smirom) g95 (GCC 4.0.3) PGI 7.1-6 (pgcc, pgf90, pgCC) Intel 9.1 (icc, ifort, icpc) Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 (cobalt) SGI MPI SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 Sun WorkShop 6 update 2 C++ 5.3 SunOS 5.10 cc: Sun C 5.8 (linew) f90: Sun Fortran 95 8.2 CC: Sun C++ 5.8 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) gcc 3.2.2 20030222 Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 IA-64 Linux 2.4.21.SuSE_309.tg1 ia64 (NCSA tg-login) gcc 3.2.2 Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 mpich-gm-1.2.6..14b-intel-r2 Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) gcc 3.4.6 20060404 Intel(R) C++ Version 10.0 Intel (R) Fortran Compiler Version 10.0 mvapich2-0.9.8p2patched-intel-ofed-1.2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) MinGW(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel SunOS5.10 64-bit n y n y y y SunOS5.10 32-bit n y n y y y IRIX64_6.5 64-bit n y y y y y IRIX64_6.5 32-bit n n n n y y Windows XP n y(15) n(15) y y y Windows XP x64 n y(15) n(15) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y FreeBSD 4.11 n n n y y y RedHat EL3 W (3) y(1) y(10) y(1) y y y RedHat EL3 W Intel (3) n y n y y n RedHat EL3 W PGI (3) n y n y y n SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y SuSe x86_64 Int (3,12) n y(13) n y y n SuSe x86_64 PGI (3,12) n y(8) n y y y Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y n Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Linux 2.6 RHEL C Lustre Intel (5) y(4) y y(4) y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 64-bit y y y y Solaris2.10 32-bit y y y y IRIX64_6.5 64-bit y y n y IRIX64_6.5 32-bit y dna y y Windows XP y y(15) y y Windows XP x64 y y(15) y y Windows Vista y n n y Mac OS X 10.3 y n FreeBSD 4.11 y n y y RedHat EL3 W (3) y y(10) y y RedHat EL3 W Intel (3) y y y n RedHat EL3 W PGI (3) y y y n SuSe x86_64 W GNU (3,12) y y y y SuSe x86_64 W Int (3,12) y y y n SuSe x86_64 W PGI (3,12) y y y n Linux 2.4 Xeon C Lustre Intel (6) y y y n Linux 2.4 SuSE ia64 C Intel (7) y y y n Linux 2.4 SGI Altix ia64 Intel y n Linux 2.6 RHEL C Lustre Intel (5) y y y n Cray XT3 2.0.41 n n n n n Notes: (1) Using mpich2 1.0.6. (2) Using mpich2 1.0.7. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Using mvapich2 0.9.8. (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 (9) With Compaq Visual Fortran 6.6c compiler. (10) With PGI and Absoft compilers. (11) PGI and Intel compilers for both C and Fortran (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is expected to fail and exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. To bypass this problem for now, change the following lines in the tools/h5ls/testh5ls.sh. ======== Original ========= # The following combination of arguments is expected to return an error message # and return value 1 TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Skip the test ========= echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== end of bypass ======== AKC - 2008/05/28 * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases: 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, change the following line in your code H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel tests failed with MPI-IO file locking message. AKC - 2007/6/25 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * Configuring with --enable-debug=all produces compiler errors on most platforms: Users who want to run HDF5 in debug mode should use --enable-debug rather than --enable-debug=all to enable debugging information on most modules. * On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long double to (unsigned) long long and from (unsigned) long long to long double. * On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 optimization flag. * On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter supports only the IEEE standard for floating-point data; it cannot be applied to HDF5 data generated on VAX. * On Cray X1, a lone colon on the command line of h5dump --xml (as in the testh5dumpxml.sh script) is misinterpereted by the operating system and causes an error. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD Opteron processor, there is a bug in the compiler for optimization(-O2). The library failed in several tests, all related to the MULTI driver. The problem has been reported to the vendor. * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platforms for serial mode. The parallel mode works fine with this option. It is suggested that you do not use this option on these platforms during configuration. * With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during compilation. The ANSI version of the compiler complains about not being able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' This warning is innocuous and can be safely ignored. * The ./dsets tests fail on the TFLOPS machine if the test program, dsets.c, is compiled with the -O option. The HDF5 library still works correctly with the -O option. The test program works fine if it is compiled with -O1 or -O0. Only -O (same as -O2) causes the test program to fail. * Not all platforms behave correctly with Szip's shared libraries. Szip is disabled in these cases, and a message is relayed at configure time. Static libraries should be working on all systems that support Szip and should be used when shared libraries are unavailable. There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * On some platforms that use Intel and Absoft compilers to build the HDF5 Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 complaining about the exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error). * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. * On at least one system, SDSC DataStar, the scheduler (in this case LoadLeveler) sends job status updates to standard error when you run any executable that was compiled with the parallel compilers. This causes problems when running "make check" on parallel builds, as many of the tool tests function by saving the output from test runs, and comparing it to an exemplar. The best solution is to reconfigure the target system so it no longer inserts the extra text. However, this may not be practical. In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to the configure and build. This will cause "make check" to continue after detecting errors in the tool tests. However, in the case of SDSC DataStar, it also leaves you with some 150 "failed" tests to examine by hand. A second solution is to write a script to run serial tests and filter out the text added by the scheduler. A sample script used on SDSC DataStar is given below, but you will probably have to customize it for your installation. Observe that the basic idea is to insert the script as the first item on the command line which executes the the test. The script then executes the test and filters out the offending text before passing it on. #!/bin/csh set STDOUT_FILE=~/bin/serial_filter.stdout set STDERR_FILE=~/bin/serial_filter.stderr rm -f $STDOUT_FILE $STDERR_FILE ($* > $STDOUT_FILE) >& $STDERR_FILE set RETURN_VALUE=$status cat $STDOUT_FILE tail +3 $STDERR_FILE exit $RETURN_VALUE You get the HDF5 make files and test scipts to execute your filter script by setting the environment variable "RUNSERIAL" to the full path of the script prior to running configure for parallel builds. Remember to "unsetenv RUNSERIAL" before running configure for a serial build. Note that the RUNSERIAL environment variable exists so that we can prefix serial runs as necessary on the target system. On DataStar, no prefix is necessary. However on an MPICH system, the prefix might have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to get the serial tests to run at all. In such cases, you will have to include the regular prefix in your filter script. * H5Ocopy() does not copy reg_ref attributes correctly when shared-message is turn on. The value of the reference in the destination attriubte is wrong. This H5Ocopy problem will affect the h5copy tool. * In the C++ API, it appears that there are bugs in Attribute::write/read and DataSet::write/read for fixed- and variable-len strings. The problems are being worked on and a patch will be provided when the fixes are available. %%%%1.8.0%%%% HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between the HDF5-1.6.x release series and HDF5 1.8.0, and contains information on the platforms tested and known problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt file in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.0 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.0 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.0 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in 1.8.0, including brief general descriptions of some new and modified APIs, are described in the "What's New in 1.8.0?" document: http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html All new and modified APIs are listed in detail in the "HDF5 Software Changes from Release to Release" document, in the section "Release 1.8.0 (current release) versus Release 1.6.x": http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Removed Feature - Support for new platforms and languages - Bug Fixes since HDF5-1.6.0 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ HDF5 Release 1.8.0 is a major release with many changes and new features. New format and interface features discussed in the "What's New in HDF5 1.8.0" document include the following: Enhanced group object management Enhanced attribute management and more efficient meta data handling Expanded datatype features Creation order tracking and indexing Improved meta data caching and cache control UTF-8 encoding New I/O filters: n-bit and scale+offset compression New link (H5L) and object (H5O) interfaces and features External and user-defined links New high-level APIs: HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS) C++ and Fortran interfaces for older high-level APIs: H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB) New and improved tools And more... http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html New APIs associated with these features, other interface changes (e.g., ENUM and struct definitions), and new library configuration flags are listed in the "Release 1.8.0 (current release) versus Release 1.6.x" section of "HDF5 Software Changes from Release to Release." http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html Compatibility ------------- Many HDF5 users and user communities have existing applications that they may wish to port to Release 1.8.0. Alternatively, some users may wish to take advantage of Release 1.8.0's improved performance without having to port such applications. To facilitate managing application compatibility and porting applications from release to release, the HDF Team has implemented the following features: Individually-configurable macros that selectively map common interface names to the old and new interfaces Library configuration options to configure the macro mappings Two related documents accompany this release: "API Compatibility Macros in HDF5" discusses the specifics of the new individually-configurable macros and library configuration options. http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html "New Features in HDF5 Release 1.8.0 and Backward/Forward Format Compatibility Issues" discusses each new feature with regard to its impact on format compatibility. http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html Referenced documents -------------------- http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html "What's New in HDF5 1.8.0" http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html The "Release 1.8.0 (current release) versus Release 1.6.x " section in "HDF5 Software Changes from Release to Release" http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html "API Compatibility Macros in HDF5" http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html "New Features in HDF5 Release 1.8.0 and Backward/Forward Format Compatibility Issues" Removed Feature =============== The stream virtual file driver (H5FD_STREAM) have been removed in this release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream and the constant H5FD_STREAM. This virtual file driver will be available at http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release, the transition is still in progress; the necessary integration tools may not be available when HDF5 Release 1.8.0 first comes out. Support for New Platforms, Languages, and Compilers =================================================== - Support for Open VMS 7.3 was added. Bug Fixes since HDF5-1.6.0 ========================== This release contains numerous bug fixes. For details, see the "Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for this release. Platforms Tested ================ The following platforms and compilers have been tested for for this release. AIX 5.2 (32/64 bit) xlc 8.0.0.11 xlC 8.0 xlf 10.01.0000.0 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.7 FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20070620 FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20080123 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9 (RHEL4) Intel 10.0 compilers (abe.ncsa.uiuc.edu) Linux 2.4.21-47 gcc 3.2.3 20030502 (osage) Linux 2.6.9-42.0.10 gcc 3.4.6 20060404 (kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC) Intel 9.1 (icc, ifort, icpc) Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, (smirom) g95 (GCC 4.0.3) PGI 6.2-5 (pgcc, pgf90, pgCC) Intel 9.1 (icc, iort, icpc) Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 (cobalt) SGI MPI SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 Sun WorkShop 6 update 2 C++ 5.3 SunOS 5.10 cc: Sun C 5.8 (linew) f90: Sun Fortran 95 8.2 CC: Sun C++ 5.8 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) gcc 3.2.2 20030222 Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 IA-64 Linux 2.4.21.SuSE_292.til1 ia64 (NCSA tg-login) gcc 3.2.2 Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 mpich-gm-1.2.5..10-intel-r2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) MinGW(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD HP Fortran V7.6-3276 Compaq C++ V6.5-004 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release x = not working in this release dna = does not apply ( ) = footnote appears below second table = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel SunOS5.8 64-bit n y n y y y SunOS5.8 32-bit n y n y y y SunOS5.10 64-bit y(1) y n y y y SunOS5.10 32-bit y(1) y n y y y IRIX64_6.5 64-bit n y y y y y IRIX64_6.5 32-bit n n n n y y AIX-5.2 32-bit y y y y y y AIX-5.2 64-bit y y y y y y Windows XP n y(15) n(15) y y y Windows XP x64 n y(15) n(15) y y y Windows Vista n n n y y y Mac OS X 10.4 PowerPC n n Mac OS X 10.4 Intel n y n y y y FreeBSD 4.11 n n n y y y RedHat EL3 W (3) y(1a) y(10) y(1a) y y y RedHat EL3 W Intel (3) n y n y y n RedHat EL3 W PGI (3) n y n y y n SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y SuSe x86_64 Int (3,12) n y(13) n y y n SuSe x86_64 PGI (3,12) n y(8) n y y y Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y n Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Alpha OpenVMS 7.3.2 n y n y n n Platform Shared Shared Shared static- Thread- C libs F90 libs C++ libs exec safe Solaris2.8 64-bit y y y x y Solaris2.8 32-bit y y y x y Solaris2.10 64-bit y x y Solaris2.10 32-bit y x y IRIX64_6.5 64-bit y y n y y IRIX64_6.5 32-bit y dna y y y AIX-5.2 & 5.3 32-bit n n n y n AIX-5.2 & 5.3 64-bit n n n y n Windows XP y y(15) y y y Windows XP x64 y y(15) y y y Windows Vista y n n y y Mac OS X 10.3 y y n FreeBSD 4.11 y n y y y RedHat EL3 W (3) y y(10) y y y RedHat EL3 W Intel (3) y y y y n RedHat EL3 W PGI (3) y y y y n SuSe x86_64 W GNU (3,12) y y y y y SuSe x86_64 W Int (3,12) y y y y(14) n SuSe x86_64 W PGI (3,12) y y y y(14) n Linux 2.4 Xeon C Lustre Intel (6) y y y y n Linux 2.4 SuSE ia64 C Intel (7) y y y y n Linux 2.4 SGI Altix ia64 Intel y y n Alpha OpenVMS 7.3.2 n n n y n Notes: (1) Using mpich 1.2.6. (1a) Using mpich2 1.0.6. (2) Using mpt and mpich 1.2.6. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 (9) With Compaq Visual Fortran 6.6c compiler. (10) With PGI and Absoft compilers. (11) PGI and Intel compilers for both C and Fortran (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases: 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, change the following line in your code H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel tests failed with MPI-IO file locking message. AKC - 2007/6/25 * On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass when run against the parallel library; the parallel tests also pass, but with lots of non-fatal error messages. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with Attributes" test. * Configuring with --enable-debug=all produces compiler errors on most platforms: Users who want to run HDF5 in debug mode should use --enable-debug rather than --enable-debug=all to enable debugging information on most modules. * On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long double to (unsigned) long long and from (unsigned) long long to long double. * On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 optimization flag. * On VAX, the Scaleoffset filter is not supported. The filter cannot be applied to HDF5 data generated on VAX. The Scaleoffset filter only supports the IEEE standard for floating-point data. * On Cray X1, a lone colon on the command line of h5dump --xml (as in the testh5dumpxml.sh script) is misinterpereted by the operating system and causes an error. * On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and the application asks to do collective IO, we have found that when using 4 processors, a simple collective write will sometimes be hung. This can be verified with t_mpi test under testpar. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculating code of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/6/30 * For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD Opteron processor, there is a bug in the compiler for optimization(-O2). The library failed in several tests, all related to the MULTI driver. The problem has been reported to the vendor. * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. Set the environment variable MP_INFOLEVEL to 0 to minimize the messages and run the tests again. The tests may fail with messages like "The socket name is already in use", but HDF5 does not use sockets. This failure is due to problems with the poe command trying to set up the debug socket. To resolve this problem, check to see whether there are many old /tmp/s.pedb.* files staying around. These are sockets used by the poe command and left behind due to failed commands. First, ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on IBM SP2 platform for the serial mode. The parallel mode works fine with this option. It is suggested that you do not use this option on these platforms during configuration. * With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during compilation. The ANSI version of the compiler complains about not being able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' This warning is innocuous and can be safely ignored. * The ./dsets tests fail on the TFLOPS machine if the test program, dsets.c, is compiled with the -O option. The HDF5 library still works correctly with the -O option. The test program works fine if it is compiled with -O1 or -O0. Only -O (same as -O2) causes the test program to fail. * Not all platforms behave correctly with Szip's shared libraries. Szip is disabled in these cases, and a message is relayed at configure time. Static libraries should be working on all systems that support Szip and should be used when shared libraries are unavailable. There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * On some platforms that use Intel and Absoft compilers to build the HDF5 Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 complaining about the exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error). * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. * On at least one system, SDSC DataStar, the scheduler (in this case LoadLeveler) sends job status updates to standard error when you run any executable that was compiled with the parallel compilers. This causes problems when running "make check" on parallel builds, as many of the tool tests function by saving the output from test runs, and comparing it to an exemplar. The best solution is to reconfigure the target system so it no longer inserts the extra text. However, this may not be practical. In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to the configure and build. This will cause "make check" to continue after detecting errors in the tool tests. However, in the case of SDSC DataStar, it also leaves you with some 150 "failed" tests to examine by hand. A second solution is to write a script to run serial tests and filter out the text added by the scheduler. A sample script used on SDSC DataStar is given below, but you will probably have to customize it for your installation. Observe that the basic idea is to insert the script as the first item on the command line which executes the the test. The script then executes the test and filters out the offending text before passing it on. #!/bin/csh set STDOUT_FILE=~/bin/serial_filter.stdout set STDERR_FILE=~/bin/serial_filter.stderr rm -f $STDOUT_FILE $STDERR_FILE ($* > $STDOUT_FILE) >& $STDERR_FILE set RETURN_VALUE=$status cat $STDOUT_FILE tail +3 $STDERR_FILE exit $RETURN_VALUE You get the HDF5 make files and test scipts to execute your filter script by setting the environment variable "RUNSERIAL" to the full path of the script prior to running configure for parallel builds. Remember to "unsetenv RUNSERIAL" before running configure for a serial build. Note that the RUNSERIAL environment variable exists so that we can can prefix serial runs as necessary on the target system. On DataStar, no prefix is necessary. However on an MPICH system, the prefix might have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to get the serial tests to run at all. In such cases, you will have to include the regular prefix in your filter script. * H5Ocopy() does not copy reg_ref attributes correctly when shared-message is turn on. The value of the reference in the destination attriubte is wrong. This H5Ocopy problem will affect the h5copy tool.